key: cord-0004383-ceorbnfz authors: Nicholson, Tracy L.; Bayles, Darrell O.; Shore, Sarah M. title: Complete Genome Sequence of Bordetella bronchiseptica Strain KM22 date: 2020-01-23 journal: Microbiol Resour Announc DOI: 10.1128/mra.01207-19 sha: 8f8eb4f004c2002face0723f2f58cc411954d36e doc_id: 4383 cord_uid: ceorbnfz Bordetella bronchiseptica isolate KM22 has been used in experimental infections of swine as a model of clinical B. bronchiseptica infection and to study host-to-host transmission. The draft genome sequence of KM22 was reported in 2014. Here, we report the complete genome sequence of KM22. 20-kb insert library preparation protocol (https://www.pacb.com/wp-content/uploads/ Procedure-Checklist-20-kb-Template-Preparation-Using-BluePippin-Size-Selection -System.pdf). The 20-kb library was sequenced with a PacBio RS II platform using two single-molecule real-time (SMRT) cells, resulting in 283,436 total reads and an average read length of 7,600 bp. Reads were subsequently assessed for quality using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Whole-genome assemblies were generated using PacBio SMRT Analysis v. 2.3.0 and Canu v. 1.5 (28) software. The average PacBio coverage for the assembled genome was 475ϫ. Assembling the PacBio data resulted in a fully sequenced closed circular chromosome, which was subsequently oriented to start at the dnaA gene and trimmed by removing any overlapping sequence. The genome was then polished and error corrected using the Broad Institute's Pilon v. 1.18 software (29) along with the Illumina GAIIx 3,474,442 paired-end sequencing reads, which were previously used for the draft assembly (26) . Default parameters were used for all software. The closed KM22 genome was then annotated using NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) (30) . The complete genome of KM22 consists of 5,205,646 bp with a GϩC content of 68.2%, a total of 4,827 predicted protein coding sequences (CDSs), 9 rRNA operons, 1 transfermessenger RNA (tmRNA), 3 noncoding RNAs (ncRNAs), and 56 tRNAs. Data availability. The whole-genome sequence for Bordetella bronchiseptica isolate KM22 was deposited in DDBJ/ENA/GenBank under the accession number CP022962. The PacBio read data were deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA398562 and SRA study accession number SRP222122 (run numbers SRR10134673 and SRR10134672). Illumina HiSeq short read sequences have been deposited at the European Nucleotide Archive under accession number ERS027415. We thank the Yale University Center for Genome Analysis for their assistance in producing the PacBio sequence data. Funding for this research was provided by the USDA Agricultural Research Service. Funding sources did not impact study design, data collection, data analysis, decisions on publication, or preparation of the manuscript. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. The bordetellae: lessons from genomics Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species Ecological sources of zoonotic diseases Risk factors for human disease emergence The BvgASR virulence regulon of Bordetella pertussis Pertussis pathogenesis-what we know and what we don't know Pertussis disease and transmission and host responses: insights from the baboon model of pertussis Biology of Bordetella bronchiseptica Bordetellosis Optimized ribotyping protocol applied to Hungarian Bordetella bronchiseptica isolates: identification of two novel ribotypes Novel genetic and phenotypic heterogeneity in Bordetella bronchiseptica pertactin Prior infection with Bordetella bronchiseptica increases nasal colonization by Haemophilus parasuis in swine Experimental airborne transmission of porcine reproductive and respiratory syndrome virus and Bordetella bronchiseptica Coinfection of pigs with porcine respiratory coronavirus and Bordetella bronchiseptica Effects of intranasal inoculation of porcine reproductive and respiratory syndrome virus, Bordetella bronchiseptica, or a combination of both organisms in pigs Effects of intranasal inoculation with Bordetella bronchiseptica, porcine reproductive and respiratory syndrome virus, or a combination of both organisms on subsequent infection with Pasteurella multocida in pigs Expression of the dermonecrotic toxin by Bordetella bronchiseptica is not necessary for predisposing to infection with toxigenic Pasteurella multocida Role of the dermonecrotic toxin of Bordetella bronchiseptica in the pathogenesis of respiratory disease in swine Influenza virus coinfection with Bordetella bronchiseptica enhances bacterial colonization and host responses exacerbating pulmonary lesions Contribution of Bordetella bronchiseptica filamentous hemagglutinin and pertactin to respiratory disease in swine The Bordetella bronchiseptica type III secretion system is required for persistence and disease severity but not transmission in swine Phenotypic modulation of the virulent Bvg phase is not required for pathogenesis and transmission of Bordetella bronchiseptica in swine The Bordetella Bps polysaccharide is required for biofilm formation and enhances survival in the lower respiratory tract of swine Draft genome sequence of the Bordetella bronchiseptica swine isolate KM22 A simple chemically defined medium for the production of phase I Bordetella pertussis Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement NCBI Prokaryotic Genome Annotation Pipeline